Atomistry » Sodium » PDB 4f5r-4foi » 4fkb
Atomistry »
  Sodium »
    PDB 4f5r-4foi »
      4fkb »

Sodium in PDB 4fkb: An Organic Solvent Tolerant Lipase 42

Enzymatic activity of An Organic Solvent Tolerant Lipase 42

All present enzymatic activity of An Organic Solvent Tolerant Lipase 42:
3.1.1.3;

Protein crystallography data

The structure of An Organic Solvent Tolerant Lipase 42, PDB code: 4fkb was solved by R.N.Zaliha, R.A.Rahman, M.S.Khusaini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.22
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.824, 81.001, 99.529, 90.00, 96.69, 90.00
R / Rfree (%) 12.7 / 16.5

Other elements in 4fkb:

The structure of An Organic Solvent Tolerant Lipase 42 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the An Organic Solvent Tolerant Lipase 42 (pdb code 4fkb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the An Organic Solvent Tolerant Lipase 42, PDB code: 4fkb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 4fkb

Go back to Sodium Binding Sites List in 4fkb
Sodium binding site 1 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:26.2
occ:1.00
 O A:HOH693 2.0 21.2 1.0
O A:LYS329 2.3 10.6 1.0
O A:HOH766 2.5 38.0 1.0
O A:SER332 2.5 15.6 1.0
O A:HOH861 2.7 80.6 1.0
O A:HOH826 2.9 1.0 1.0
C A:LYS329 3.5 8.7 1.0
C A:SER332 3.6 13.2 1.0
N A:SER332 3.8 11.0 1.0
O A:HOH639 3.9 27.9 1.0
CA A:LYS329 4.1 8.5 1.0
CA A:SER332 4.1 11.3 1.0
O A:HOH859 4.2 47.2 1.0
O A:HOH531 4.3 16.7 1.0
N A:GLY331 4.5 10.6 1.0
O A:HOH860 4.5 89.0 1.0
CB A:SER332 4.5 10.6 1.0
N A:ARG330 4.6 9.1 1.0
O A:HOH827 4.6 40.8 1.0
N A:SER333 4.7 13.7 1.0
CA A:ARG330 4.8 8.7 0.5
CB A:LYS329 4.8 8.9 1.0
C A:GLY331 4.8 10.0 1.0
CA A:ARG330 4.9 8.6 0.5
C A:ARG330 4.9 9.7 1.0

Sodium binding site 2 out of 9 in 4fkb

Go back to Sodium Binding Sites List in 4fkb
Sodium binding site 2 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:25.9
occ:1.00
 O A:HOH578 2.1 21.5 1.0
O A:THR272 2.2 9.6 1.0
O A:HOH760 2.3 35.9 1.0
OE1 A:GLU270 2.4 9.5 1.0
OE2 A:GLU284 2.8 12.8 1.0
O A:HOH577 3.0 22.6 1.0
O A:HOH684 3.0 26.2 1.0
NA A:NA406 3.2 64.9 1.0
CD A:GLU270 3.2 9.7 1.0
OE2 A:GLU270 3.4 11.7 1.0
C A:THR272 3.4 8.0 1.0
O A:HOH743 3.4 34.9 1.0
CD A:GLU284 3.6 9.6 1.0
N A:THR272 3.7 6.9 1.0
O A:HOH742 4.0 33.0 1.0
ND2 A:ASN355 4.2 9.8 1.0
CA A:THR272 4.2 7.4 1.0
OE1 A:GLU284 4.3 8.6 1.0
N A:TYR273 4.3 6.9 1.0
CG A:GLU284 4.4 7.4 1.0
CA A:TYR273 4.4 7.7 1.0
CG A:GLU270 4.6 9.1 1.0
C A:ARG271 4.6 5.7 1.0
O A:HOH586 4.6 20.5 1.0
CA A:ARG271 4.9 5.8 1.0
OE2 A:GLU315 4.9 16.4 1.0
CG A:ASN355 5.0 9.5 1.0

Sodium binding site 3 out of 9 in 4fkb

Go back to Sodium Binding Sites List in 4fkb
Sodium binding site 3 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:64.9
occ:1.00
 O A:HOH742 2.1 33.0 1.0
O A:HOH743 2.2 34.9 1.0
O A:HOH760 2.4 35.9 1.0
O A:HOH578 2.4 21.5 1.0
O A:HOH967 2.8 45.7 1.0
NA A:NA405 3.2 25.9 1.0
O A:HOH684 3.9 26.2 1.0
OE2 A:GLU270 4.1 11.7 1.0
O A:HOH577 4.4 22.6 1.0
O A:HOH942 4.7 34.2 1.0
OE1 A:GLU270 4.7 9.5 1.0
CD A:GLU270 4.7 9.7 1.0
OE2 A:GLU284 4.7 12.8 1.0
O A:HOH749 4.9 29.2 1.0
O A:THR272 5.0 9.6 1.0

Sodium binding site 4 out of 9 in 4fkb

Go back to Sodium Binding Sites List in 4fkb
Sodium binding site 4 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:37.7
occ:1.00
 OE1 A:GLU202 2.0 20.0 1.0
CL A:CL417 2.2 14.6 1.0
CD A:GLU202 2.6 20.0 1.0
CG A:ARG214 2.8 18.8 1.0
N A:ARG215 3.2 11.2 1.0
OE2 A:GLU202 3.2 20.0 1.0
O A:HOH525 3.3 12.7 1.0
CG A:GLU202 3.6 20.0 1.0
CD A:ARG214 3.7 30.3 1.0
CB A:ARG215 3.8 11.7 1.0
O A:ARG215 3.8 20.4 1.0
CB A:ARG214 3.9 13.8 1.0
CA A:ARG214 3.9 11.3 1.0
C A:ARG214 4.0 12.0 1.0
CA A:ARG215 4.0 11.8 1.0
O A:HOH753 4.1 28.9 1.0
O A:HOH538 4.3 13.4 1.0
C A:ARG215 4.4 15.4 1.0
OD1 A:ASP205 4.4 11.5 1.0
CA A:ASP205 4.7 10.3 1.0
OH A:TYR224 4.7 10.6 1.0
NE A:ARG214 4.8 53.1 1.0
O A:TYR204 4.9 12.6 1.0
CG A:ASP205 4.9 11.8 1.0
N A:PHE206 5.0 9.5 1.0

Sodium binding site 5 out of 9 in 4fkb

Go back to Sodium Binding Sites List in 4fkb
Sodium binding site 5 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:26.9
occ:1.00
 O B:HOH816 2.1 43.5 1.0
O B:HOH730 2.1 25.1 1.0
O B:LYS329 2.3 13.7 1.0
O B:HOH757 2.4 41.3 1.0
O B:SER332 2.4 14.7 1.0
C B:LYS329 3.5 10.8 1.0
C B:SER332 3.6 12.0 1.0
N B:SER332 3.8 10.9 1.0
O B:HOH791 4.0 34.9 1.0
CA B:LYS329 4.1 9.6 1.0
CA B:SER332 4.1 11.4 1.0
O B:HOH934 4.3 48.9 1.0
O B:HOH580 4.3 18.6 1.0
O B:HOH745 4.4 61.0 1.0
O B:HOH741 4.4 46.2 1.0
O B:HOH815 4.5 42.7 1.0
N B:GLY331 4.5 11.2 1.0
CB B:SER332 4.5 12.0 1.0
N B:ARG330 4.5 11.8 1.0
N B:SER333 4.7 14.3 1.0
C B:GLY331 4.8 9.8 1.0
CB B:LYS329 4.8 9.3 1.0
CA B:ARG330 4.8 11.8 1.0
C B:ARG330 4.9 10.1 1.0

Sodium binding site 6 out of 9 in 4fkb

Go back to Sodium Binding Sites List in 4fkb
Sodium binding site 6 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:40.9
occ:1.00
 O B:HOH910 2.1 46.0 1.0
O B:HOH575 2.5 20.0 1.0
OG B:SER369 2.5 14.4 0.6
O B:HOH724 2.7 29.1 1.0
CB B:SER369 3.4 14.4 0.4
CB B:SER369 3.5 13.8 0.6
O B:SER369 4.0 15.6 1.0
O B:ASN355 4.1 8.9 1.0
C B:SER369 4.2 12.9 1.0
O A:HOH739 4.2 50.5 1.0
OD1 B:ASN355 4.3 11.6 1.0
OG B:SER369 4.4 19.1 0.4
O B:HOH662 4.4 39.4 1.0
CA B:SER369 4.4 12.7 0.4
CA B:SER369 4.5 12.2 0.6
ND2 B:ASN367 4.6 11.3 1.0
N B:PHE370 4.6 11.7 1.0
OD1 B:ASN367 4.6 10.7 1.0
CG B:ASN355 5.0 7.5 1.0

Sodium binding site 7 out of 9 in 4fkb

Go back to Sodium Binding Sites List in 4fkb
Sodium binding site 7 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:31.9
occ:1.00
 O B:THR272 2.2 11.7 1.0
O B:HOH726 2.2 22.7 1.0
OE1 B:GLU270 2.4 12.8 1.0
O B:HOH621 2.6 25.6 1.0
O B:HOH653 2.7 21.7 1.0
O B:HOH900 2.8 52.8 1.0
OE2 B:GLU284 3.1 12.7 1.0
CD B:GLU270 3.2 9.6 1.0
C B:THR272 3.4 8.9 1.0
OE2 B:GLU270 3.4 14.3 1.0
N B:THR272 3.9 9.0 1.0
CD B:GLU284 3.9 9.9 1.0
O B:HOH899 4.0 36.5 1.0
CA B:THR272 4.3 8.4 1.0
N B:TYR273 4.4 7.9 1.0
ND2 B:ASN355 4.5 8.6 1.0
CG B:GLU270 4.5 10.3 1.0
CA B:TYR273 4.5 8.2 1.0
OE1 B:GLU284 4.6 10.0 1.0
OE2 B:GLU315 4.6 20.2 1.0
CG B:GLU284 4.6 8.1 1.0
C B:ARG271 4.8 7.5 1.0
OG1 B:THR272 4.9 19.3 1.0
O B:HOH657 4.9 23.7 1.0

Sodium binding site 8 out of 9 in 4fkb

Go back to Sodium Binding Sites List in 4fkb
Sodium binding site 8 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:42.4
occ:1.00
 O B:HOH918 2.2 44.4 1.0
O B:HOH929 2.4 50.9 1.0
O A:HOH884 2.5 33.1 1.0
O A:HOH727 2.6 23.9 1.0
O B:HOH746 2.6 22.5 1.0
O A:HOH642 4.1 22.3 1.0
O B:HOH921 4.1 42.6 1.0
O A:ALA83 4.2 11.6 1.0
ND2 B:ASN280 4.2 16.8 1.0
O B:HOH919 4.2 34.3 1.0
OH B:TYR282 4.5 10.5 1.0
O A:HOH906 4.9 47.3 1.0

Sodium binding site 9 out of 9 in 4fkb

Go back to Sodium Binding Sites List in 4fkb
Sodium binding site 9 out of 9 in the An Organic Solvent Tolerant Lipase 42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of An Organic Solvent Tolerant Lipase 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:12.7
occ:1.00
 O B:HOH733 2.3 25.1 1.0
O B:HOH519 2.3 8.6 1.0
O B:ALA192 2.3 7.8 1.0
O B:HOH543 2.4 9.2 1.0
CB B:ALA192 3.4 7.6 1.0
C B:ALA192 3.4 7.9 1.0
CA B:ALA192 4.0 7.1 1.0
O B:ALA191 4.4 7.7 1.0
N B:VAL193 4.6 6.7 1.0
O B:HOH566 4.7 8.7 1.0
CA B:VAL193 5.0 6.8 1.0

Reference:

R.N.Zaliha, R.N.Rahman, M.S.Khusaini. An Organic Solvent Tolerant Lipase 42 To Be Published.
Page generated: Mon Oct 7 15:23:41 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy